Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012471224.1 GLOV_RS15795 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_000020385.1:WP_012471224.1 Length = 475 Score = 493 bits (1268), Expect = e-144 Identities = 248/473 (52%), Positives = 329/473 (69%), Gaps = 1/473 (0%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M F+ VIGLEVHV+LKTDSK+F FGAEPN NT + LA PG LPV+N++ V++A+ Sbjct: 1 MRFQPVIGLEVHVQLKTDSKIFCGCSTRFGAEPNLNTCPVCLALPGALPVLNQKVVEFAI 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITR 120 A +A N I+ + F RKNYFYPD PK YQISQFD PI G++DI V +TKRIGITR Sbjct: 61 MAGLATNCSISPTNIFARKNYFYPDLPKGYQISQFDLPICLAGHLDIAVGDQTKRIGITR 120 Query: 121 LHMEEDAGKSTH-KGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179 +HMEEDAGK H +G S VDLNR GTPL+E+VSEPD+R+ EA AYL+KL I+ Y G+ Sbjct: 121 IHMEEDAGKLVHGQGGGSGVDLNRAGTPLLEVVSEPDMRTADEAVAYLKKLYQIVTYLGI 180 Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239 D MEEGS RCDAN+S+ P G FGT+AE+KN+NSF +V+ +EYE RQ E + GG Sbjct: 181 CDGNMEEGSFRCDANVSVMPVGSGTFGTRAEIKNVNSFKFVKAAIEYEIARQCELIEDGG 240 Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299 ++ QETR FD + G T MR KE + DYRYFP+PD+VP+ I D W +RV+ +PELP+ + Sbjct: 241 KVVQETRLFDPNKGVTRSMRGKEEAHDYRYFPDPDLVPVVISDDWIKRVKNELPELPEVK 300 Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359 +++ E LP YDA VLT ++ ++D+FE + + K +NW+MG + LN N + + Sbjct: 301 FNRFLTEYSLPEYDADVLTSSRPLADYFEQCAQTCNNAKAAANWVMGELTRSLNDNGIAI 360 Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419 D+ ++P LAG+IKLI+ GT+S IAKKVF +L GG A I+E GL Q+SD + Sbjct: 361 EDSPVSPAQLAGLIKLIDGGTISGTIAKKVFEDLWKNGGEAAAIVEQQGLAQVSDTGAIE 420 Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472 +++ + N VE+Y+ GK K GF VGQ+MKA KG+ANP +VN LLKQ+L Sbjct: 421 TAIDQIMAANMGQVEEYRGGKDKVFGFFVGQVMKAMKGKANPAVVNDLLKQKL 473 Lambda K H 0.313 0.133 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 668 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 475 Length of database: 475 Length adjustment: 33 Effective length of query: 442 Effective length of database: 442 Effective search space: 195364 Effective search space used: 195364 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 bits)
Align candidate WP_012471224.1 GLOV_RS15795 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00133.hmm # target sequence database: /tmp/gapView.18364.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-187 608.0 0.0 6e-187 607.8 0.0 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012471224.1 GLOV_RS15795 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012471224.1 GLOV_RS15795 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 607.8 0.0 6e-187 6e-187 3 480 .. 2 473 .. 1 474 [. 0.99 Alignments for each domain: == domain 1 score: 607.8 bits; conditional E-value: 6e-187 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 ++ viGlEvHvql t sK+Fc cs+++ +pN n+cpvcl+lPGalPvlN+++v++A++ +la+n+ lcl|NCBI__GCF_000020385.1:WP_012471224.1 2 RFQPVIGLEVHVQLKTDSKIFCGCSTRFGA-EPNLNTCPVCLALPGALPVLNQKVVEFAIMAGLATNCS 69 67889***********************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140 +s++ +F+RK+YfYpDlPkgyqi+q+dlPi+ G+l+i + ++ k+igi+r+h+EeD+gk+++ + lcl|NCBI__GCF_000020385.1:WP_012471224.1 70 -ISPTNIFARKNYFYPDLPKGYQISQFDLPICLAGHLDIAVGDQTKRIGITRIHMEEDAGKLVHGQGG- 136 .779**********************************************************999665. PP TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209 s vD+NR+g+PLlE+V++Pd+++a+ea+a+lkkl qi+ yl+i dg++eeGs+R+D+Nvs+ ++G+ lcl|NCBI__GCF_000020385.1:WP_012471224.1 137 --GSGVDLNRAGTPLLEVVSEPDMRTADEAVAYLKKLYQIVTYLGICDGNMEEGSFRCDANVSVMPVGS 203 ..89***************************************************************** PP TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278 ++gtr+EiKN+ns+k +++aieyEi+Rq +l+++g +v+qetr fd +k +t s+R Kee++DYRYfp lcl|NCBI__GCF_000020385.1:WP_012471224.1 204 GTFGTRAEIKNVNSFKFVKAAIEYEIARQCELIEDGGKVVQETRLFDPNKGVTRSMRGKEEAHDYRYFP 272 ********************************************************************* PP TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkl 347 +Pdl+p++i+++++k+ v+++lpelPe k +r+ +ey l e+da vl+s + l+d+fe+ +++ +++k+ lcl|NCBI__GCF_000020385.1:WP_012471224.1 273 DPDLVPVVISDDWIKR-VKNELPELPEVKFNRFLTEYSLPEYDADVLTSSRPLADYFEQCAQTCNNAKA 340 ****************.**************************************************** PP TIGR00133 348 avnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklg 416 a+nW++ el+++Ln++ i ++++ ++p +la likli+ g+is+++ak+++e l +n++++ +++e++g lcl|NCBI__GCF_000020385.1:WP_012471224.1 341 AANWVMGELTRSLNDNGIAIEDSPVSPAQLAGLIKLIDGGTISGTIAKKVFEDLWKNGGEAAAIVEQQG 409 ********************************************************************* PP TIGR00133 417 liqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 l q+sd+ ++ +++++++ n ++ve+y+ gk+k+++f+vGqvmk kg+a+p+ v+ llk++l lcl|NCBI__GCF_000020385.1:WP_012471224.1 410 LAQVSDTGAIETAIDQIMAANMGQVEEYRGGKDKVFGFFVGQVMKAMKGKANPAVVNDLLKQKL 473 *************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (475 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.75 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory